In my opinion, that's what Heroes are for. Trying to manually design each individual unit would add complexity to an already complex (d20) system.
Don't get me wrong, I LOVED Alpha Centauri, but their battle mechanics were MUCH simpler than any sort of d20 based system like this game is going with.
Honestly, I'm already intimidated by the ramifications of having a d20 system for every single unit in the game.